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At least 19 recordsLinked to original sources

PubMed2025

The effects of cryptic diversity on diversification dynamics analyses in Crocodylia.

Incomplete taxon sampling due to underestimation of present-day biodiversity biases diversification analysis by favouring slowdowns in speciation rates towards the recent time. For instance, in diversification dynamics studies in Crocodylia, long-term low net-diversification rates and slowdowns in speciation rates have been suggested to characterize crocodylian evolution. However, crocodylian cryptic diversity has never been considered. Here, we explore the effects of incorporating cryptic diversity into a diversification dynamics analysis of extant crocodylians. We inferred a time-calibrated cryptic-species-level phylogeny using cytochrome b sequences of 45 lineages compared with the formally recognized 26 crocodylian species. Diversification rate estimates using the cryptic-species-level phylogeny show increasing speciation and net-diversification rates towards the present time, which contrasts with previous findings. Cryptic diversity should be considered in future macroevolutionary analyses; however, the representation of cryptic extinct taxa represents a major challenge. Additionally, further investigation of crocodylian diversification dynamics under different underlying genomic data is encouraged upon advances in population genetics. Our case study adds to the diversification dynamics knowledge of extant taxa and demonstrates that cryptic species and robust taxonomic assessment are essential to study recent biodiversity dynamics with broad implications for evolutionary biology and ecology.

Animals↗

PubMed2025

Biogeographic Structure and Mitonuclear Discordance Reveal Cryptic Diversity in Pacific Herring (Clupea pallasii).

Forage fishes are biological drivers throughout the Pacific Ocean, from the Arctic to nearly subtropical latitudes. As a critical trophic link, the health and stability of Pacific herring (Clupea pallasii) populations have implications for other marine species, including several targeted by large, productive fisheries. Previous research has indicated marked divergence between Pacific herring in the Bering Sea and the Gulf of Alaska. Seeking to localize this biogeographic break, we generated low-coverage whole genome resequencing data for 120 Pacific herring from seven sites across the northern Gulf of Alaska and the eastern Bering Sea and Aleutian Islands. Single nucleotide polymorphisms across the mitogenome (267) and nuclear genome (~5.6 million) corroborate a biogeographic break in Pacific herring along the Alaska Peninsula and Aleutian Islands, as far west as Unalaska. We identified two distinct populations: one exists along the northern coasts of the Aleutian Islands and in the eastern Bering Sea; the other occupies the southern edge of the Aleutians and the Gulf of Alaska. Two mitochondrial haplogroups co-occurring across the Gulf of Alaska suggest secondary contact between two populations, likely representing glacial refugia. Our results underscore the importance of geological events to contextualize the diversification of forage fish species.

Bering Sea↗

PubMed2025

Hybridization as driving force for cryptic species diversity in the Caribbean coral genus Madracis.

Species boundaries in scleractinian corals remain highly elusive due to conflicting patterns between morphological and molecular phylogenies, often caused by morphological plasticity, occurrence of cryptic species, incomplete lineage sorting or introgressive hybridization. Here, we use an integrated systematics approach, which combines reduced representation genome sequencing (nextRAD), micro-morphometric characterization, SEM analyses and compilation of life history traits, to infer phylogenetic relationships among closely related species in the Caribbean coral genus Madracis. In total, we analyzed 235 Madracis specimens from Curaçao and Bermuda collected from 10-90 m depth. Sequence- and SNP-based analyses for 115 samples generated unprecedented species resolution in Madracis, greatly supporting the morphology-based taxonomy of the current, accepted Caribbean species M. senaria, M. decactis, M. formosa, M. carmabi and M. mirabilis (M. auretenra). The exception was M. pharensis, in which we found evidence for three separate lineages, and for which we found signatures of admixture and introgression. These three M. pharensis lineages showed distinct depth distributions (thus classified as shallow, deep and very deep) and were partially distinguishable on the basis of fine microstructural elements of the collumella, septa and coenosteum. Further taxonomic comparisons are needed to formalize these putative cryptic species. Overall, our integrated systematics approach further resolves species relationships in the Caribbean genus Madracis, supports the morphological descriptions for most of the recognized species, but also reveals the existence of cryptic diversity in groups marked by high admixture, thus suggesting hybridization as a driving force in coral species diversity.

Animals↗

PubMed2025

Integrating hotspot dynamics and centers of diversity: a review of Indo-Australian Archipelago biogeographic evolution and conservation.

The Indo-Australian Archipelago (IAA) is the world's preeminent marine biodiversity hotspot, distinguished by its exceptional species richness in tropical shallow waters. This biodiversity has spurred extensive research into its evolutionary and biogeographic origins. Two prominent theoretical frameworks dominate explanations for the IAA's biodiversity: the "centers-of hypotheses" and the "hopping hotspot hypothesis". The "centers-of hypotheses" posits that specific regions serve as key sources of IAA biodiversity, either through the accumulation and overlap of species from external areas or via elevated rates of local speciation. In contrast, the "hopping hotspot hypothesis" asserts that biodiversity hotspots are dynamic, shifting across geological timescales in response to tectonic and environmental changes. This review synthesizes these contrasting perspectives into an integrated framework, the "Dynamic Centers Hypothesis," which proposes that as biodiversity hotspots migrate over time, the IAA's role in generating and sustaining biodiversity has evolved, with varying contributions from different sources dominating distinct historical phases. By synthesizing the evidence for both hypotheses and incorporating recent findings, including fossil and phylogeography data, we propose the "Dynamic Centers Hypothesis" as a comprehensive and unifying explanation for the IAA's biodiversity. The review further explores biogeographic delineation, aligning tropical marine realms with the IAA's evolutionary trajectory, from its Tethyan roots to its modern Indo-West Pacific dominance. Looking forward, advances in DNA barcoding and genomics are uncovering vast cryptic diversity, revolutionizing our comprehension of IAA phylogeographic history. These discoveries underscore the imperative for a multidimensional conservation framework, integrating phylogenetic, and functional diversity, to preserve this biodiversity hotspot amid escalating global change.

Biogeography↗

PubMed2026

Untangling the Arisaema enigma: Investigating the complex evolutionary history and species relationships in North American Arisaema.

PREMISE: The evolutionary history of morphologically variable plant groups is often obscured by cryptic diversity, morphological convergence, and limited genetic data. Arisaema, a diverse genus within Araceae, exemplifies these challenges. Although some taxonomic treatments recognize only two species of North American Arisaema (A. dracontium and A. triphyllum), other studies have identified morphologically distinct groups within both taxa. Here, we reconstructed evolutionary relationships in North American Arisaema, assessed genetic structure and admixture, and tested the monophyly of proposed species. METHODS: We used 2b-RAD sequencing to generate genome-wide SNP data for 146 samples from 31 populations across the eastern United States. Phylogenetic relationships were inferred using maximum-likelihood and Bayesian approaches. Population structure and admixture were assessed using the program structure and principal component analysis (PCA). RESULTS: Both the Arisaema triphyllum and A. dracontium complexes formed well-supported monophyletic groups. Within the A. dracontium complex, we recovered three monophyletic lineages: A. dracontium, A. calciphilum, and A. macrospathum. In the A. triphyllum complex, A. quinatum, A. stewardsonii, and A. allegheniense consistently formed distinct groups. Relationships between A. pusillum and A. acuminatum, and among A. triphyllum s.s., A. purpurascens, and A. striatum were less clearly resolved, likely due to recent or incomplete divergence, gene flow, or polyploidy. CONCLUSIONS: The results support the monophyly of multiple newly proposed taxa within North American Arisaema, but additional sampling across the species' ranges is needed to fully resolve species boundaries. Our study provides the first evolutionary framework for this group, providing a foundation for future ecological, taxonomic, and conservation research in the genus.

Araceae↗

PubMed2026

Genome-wide insights into the evolutionary and demographic history of the red alga Mazzaella laminarioides: Evidence for speciation with ancient migration along the southeast Pacific coast.

The mechanisms driving lineage divergence in red algae remain unexplored, despite the group's remarkable diversity and ancient evolutionary history. The red alga Mazzaella laminarioides, a Chilean intertidal species complex composed of three parapatric cryptic lineages (North, Center, South), offers a valuable system to evaluate these processes, as its life history combines severe dispersal limitation with a haploid-diploid cycle that may influence the emergence of reproductive barriers. We reconstructed its evolutionary history using whole-genome sequencing and nuclear genome assembly of representative individuals from each lineage. Phylogenomic analyses based on 1,507 single-copy orthologs recovered three deeply divergent lineages with limited nuclear discordance consistent with incomplete lineage sorting. For both splits, demographic modelling was most consistent with an Ancient Migration scenario, although support over strict isolation was moderate, suggesting that divergence may have begun with low asymmetric ancestral gene flow followed by subsequent loss of connectivity, demographic bottlenecks, and later population expansion. Coding sequence analyses revealed lineage-specific dN/dS heterogeneity; only one South-lineage locus passed FDR correction (metaxin-1, mitochondrial protein import), with two further South-lineage candidates in chlorophyll and heme biosynthesis falling below the FDR threshold. Together, these signals suggest that divergent selective pressures on energy acquisition may have contributed to divergence at the southern end of the distribution. These results add to the small but growing body of whole-genome data for red algae and, alongside recent macroalgal studies, suggest that ancestral connectivity could be a recurrent feature of lineage divergence even in marine organisms with extremely restricted dispersal.

Rhodophyta↗

PubMed2025

There is gold in the graveyard: a new lineage of zombie-ant fungi in the genus Ophiocordyceps (Ophiocordycipitaceae: Hypocreales) from Minas Gerais, Brazil.

Ophiocordyceps serves as a key model for studying cryptic fungal diversity and behavioural manipulation of hymenopterous insects. Here, we describe Ophiocordyceps acanthoponerae, a newly discovered species infecting Acanthoponera mucronata (Heteroponerini: Formicidae) in a Brazilian Atlantic rainforest-Cerrado ecotone. Morphological analyses revealed mixed traits characteristic of Ophiocordyceps lineages associated with ants and wasps, including leaf biting behaviour manipulation, dark brown ascostromata covering 360º of the stalk, ascospores producing capilliconidia and hirsutelloid asexual morphs. Phylogenetic analyses based on four genomic regions (SSU, LSU, TEF and RPB1) placed this species outside the traditional myrmecophilous hirsutelloid clades O. unilateralis and O. kniphofioides, and within a novel clade closely related to the wasp pathogen O. humbertii. This discovery represents the first record of Ophiocordyceps infecting Heteroponerini and highlights an unexplored lineage of manipulative fungi. Our findings expand the known host range for myrmecophilous Ophiocordyceps and underscore the importance of studying fungal diversity in under-sampled ecological niches. Citation: Lima-Santos SJ, Araújo JPM, Feitosa RM, Mendes-Pereira T, Elliot SL, Evans HC (2025). There is gold in the graveyard: a new lineage of zombie-ant fungi in the genus Ophiocordyceps (Ophiocordycipitaceae: Hypocreales) from Minas Gerais, Brazil. Fungal Systematics and Evolution 16: 243-264. doi: 10.3114/fuse.2025.16.14.

Acanthoponera↗

PubMed2026

Promoter identity shapes splicing outcomes and fidelity.

Gene expression is a complex process subject to regulation at multiple functionally interconnected levels. One prominent example is the crosstalk between transcription and splicing regulation. Past work has shown that transcription can influence splicing in multiple ways, but a systematic investigation of this complex interplay is lacking. Here we employ massively parallel reporter assays of large combinatorial promoter-splice site libraries to dissect how promoter identity and transcription dynamics affect alternative splicing in human cells. We find that promoter identity, rather than expression level, exerts strong and highly context-specific effects on cassette exon inclusion, exceeding the effect of pharmacological inhibitors of transcription initiation or elongation. Groups of exons display coordinated promoter-dependent splicing behavior, and we identified predictive sequence and structural features underlying this sensitivity. Promoter and gene architecture also shape isoform diversity by modulating cryptic splice site usage. These findings present promoters as central regulators of splicing outcomes and fidelity.

Humans↗

PubMed2026

De Novo Assembly and Comparative Analysis of the Complete Mitochondrial Genome of Mesenchytraeus (Annelida, Enchytraeidae).

The Changbai Mountain range is one of the key glacial refugia in Northeast Asia. Mesenchytraeus exhibits high species diversity, strong endemism, and widespread cryptic species in this region, for which mitogenomes provide useful molecular markers for exploring cryptic species complexes. This makes Mesenchytraeus an ideal model for studying mitogenome evolution among closely related lineages; however, no mitogenome data have been reported for this genus to date. In this study, we performed de novo assembly, annotation, and comparative analysis of the mitogenomes of 13 Mesenchytraeus species (14 individuals) from Changbai Mountain. All mitogenomes are typical circular molecules containing 37 genes, but putative control regions are rearranged and consistently located between ATP6 and trnR. All species exhibit annelid-specific strand nucleotide biases, characterized by negative GC skew and near-zero AT skew. Codon usage analysis reveals that codon families with wobble U are significantly biased toward mtDNA codons, whereas those with wobble C or G are biased toward non-mtDNA codons, suggesting a conserved mitochondrial codon usage pattern in annelids. All tRNAs form typical cloverleaf secondary structures except trnS2, which lacks the D-stem and the dihydrouridine (DHU) arm in some species. The putative control regions commonly contain complex palindromic repeats, hairpins, and repetitive elements, and may harbor dual replication origins. Phylogenetic analyses support the monophyly of Mesenchytraeus and reveal significant molecular divergence among morphologically cryptic species. This study provides the first mitogenome dataset for Mesenchytraeus and offers new insights into the evolution and replication mechanisms of mitogenomes in Clitellata and broader Annelida.

Mesenchytraeus↗

PubMed2026

Cryptic serpentine divergence and substrate adaptation of Cardamine glauca in the Balkan Peninsula.

BACKGROUND AND AIMS: Serpentine soils represent one of the most challenging substrates for plant life due to skewed ratios of essential nutrients and toxic concentrations of metals. Plant adaptation to such conditions may lead to locally adapted edaphic ecotypes or, when reproductive barriers evolve, to distinct serpentine endemics. However, a third scenario may occur: cryptic edaphic divergence, where phenotypically similar lineages adapted to contrasting substrates exhibit deep genetic divergence. Here, we tested whether substrate-associated divergence reflects repeated serpentine adaptation or cryptic edaphic lineage divergence in Cardamine glauca (Brassicaceae) in Balkan peninsula - a hotspot of serpentine endemism in Europe. METHODS: We sampled and sequenced genomes of 43 individuals of C. glauca together with four individuals representing closely related taxa, C. plumieri and C. pancicii, from variable substrates across the Balkans. We combined phylogenomics, population genomic analyses of selection and a reciprocal transplant experiment to infer the most likely evolutionary scenario. KEY RESULTS: Phylogenomic analysis of 941 loci confirmed monophyly of C. glauca, including the local endemic C. pancicii, but revealed deep splits (∼2.2-3.2 Mya) between co-occurring serpentine and non-serpentine lineages. Population genomic analyses of replicated geographically proximate serpentine-non-serpentine population pairs demonstrated strong genome-wide differentiation and limited gene flow between edaphic types. Window-based analyses of local genomic divergence and tests for positive selection revealed candidate genes involved in ion transport, membrane transporter activity and metal homeostasis, consistent with the hypothesis of substrate-driven ecological adaptation. This was further supported by a significant substrate-of-origin fitness advantage in a reciprocal transplant experiment. CONCLUSIONS: Altogether, our results demonstrate that edaphic preferences may correspond with deep genetic divergence between similar-looking yet differently adapted lineages. The presence of cryptic edaphic lineages suggests that plant diversity may still be underestimated in genomically underexplored but edaphically diverse hotspots such as the Balkans.

Cardamine glauca↗

PubMed2026

Biosynthesis of Crinipellin Diterpenes in Mushroom Marasmius fiardii PR-910.

Crinipellins are a distinctive family of 5/5/5/5 tetracyclic diterpenoids previously reported exclusively from mushrooms of the genus Crinipellis. Despite extensive synthetic studies, the biosynthetic machinery responsible for crinipellin formation has remained elusive. Here, we identify the crinipellin biosynthetic gene cluster (mfd) from the mushroom Marasmius fiardii PR-910, a member of the family Marasmiaceae to which Crinipellis also belongs, although M. fiardii PR-910 itself has not been previously reported to produce crinipellins. Using a combination of site-directed mutagenesis guided by an AlphaFold3-generated structural model, stable isotope-labeling studies, density functional theory (DFT) calculations, and ab initio molecular dynamics (AIMD) simulations, the cyclization mechanism of the diterpene synthase MfdB, which constructs the fused tetraquinane scaffolds 1 and 2, was elucidated. Mutagenesis of MfdB uncovered cryptic cyclization pathways that generate structurally diverse diterpenes, including unprecedented bridged and rearranged diterpene skeletons (4-6), whose formation is supported by computational analyses, and further revealed an unusual arginine-rich diphosphate-binding architecture. Heterologous expression studies in Aspergillus oryzae and Saccharomyces cerevisiae established the oxidative functions of the cytochrome P450 enzymes MfdC, MfdD, and MfdE, leading to the production of 19 previously undescribed oxidized metabolites (16-34). Notably, MfdE, a member of the largely unexplored CYP_FUM15-like subfamily, catalyzes an unusual oxidative demethylation through C-C bond cleavage, expanding the known catalytic repertoire of fungal cytochrome P450 enzymes. Collectively, this work establishes the biosynthetic logic of crinipellin formation, reveals how terpene synthase plasticity generates cryptic diterpene scaffolds, and demonstrates how oxidative tailoring by multiple cytochrome P450 enzymes drives diterpene scaffold diversification.

Diterpenes↗

PubMed2026

Genome-Guided Discovery of Antimalarial 4-Amino-2,4-Pentadienoate-Containing Cyclolipodepsipeptides.

4-Amino-2,4-pentadienoate-containing cyclolipodepsipeptides (APD-CLDs) represent a structurally distinctive family of natural products known for their selective activity against hypoxic cancer cells. To explore the structural diversity of APD-CLDs, we have identified and prioritized cryptic APD-CLD biosynthetic gene clusters (BGCs) for compound discovery. Using a combination of genetic and chemical methods, we successfully activated three dormant BGCs, leading to the discovery of 12 new APD-CLDs. These newly discovered metabolites significantly expanded the diversity of the APD-CLD family, with chloromalamides and arabimalamides representing the first halogenated and glycosylated members, respectively. Unexpectedly, chloromalamides and arabimalamides exhibited potent antiplasmodial activity, with IC50 values in the 25-161 nM range against drug-sensitive and multidrug-resistant Plasmodium falciparum strains. Phenotypic studies revealed arabimalamide B halted parasite development during the asexual blood stage life cycle, resulting in enlarged digestive vacuoles, dispersed hemozoin, and ultimately reduced reinvasion efficiency. These phenotypes are reminiscent of the effect of chloroquine and other 4-aminoquinoline drugs, suggesting that arabimalamides may disrupt the parasite's heme detoxification mechanism. Biosynthetic studies identified key scaffold-forming and modifying enzymes, including a rare membrane glycosyltransferase in arabimalamide biosynthesis. Together, these findings unveil APD-CLDs as new antimalarial lead scaffolds and set the stage for structural diversification and optimization.

Antimalarials↗

PubMed2026

Molecular identification and diversity assessment of Tyrrhenian Romulea species (Iridaceae).

Taxonomic assignments based only on morphology are often insufficient for delimiting species, particularly in complexes shaped by hybridization and polyploidy, where species boundaries are unclear. This limitation hinders progress in ecological, biogeographic and conservation research. The genus Romulea, distributed across Africa and the Mediterranean Basin, exemplifies this challenge. Despite its remarkable diversity, Mediterranean Romulea has not received much attention from genetic and molecular studies. Here, we present the first multilocus genotype analysis of Mediterranean Romulea taxa, focusing on the Tyrrhenian biogeographic province. Using target-capture sequencing with the universal Angiosperms353 kit, we generated genomic data for 272 individuals representing 18 putative taxa. Our findings reveal genetic groups that align with current taxonomy, the existence of cryptic divergence, and highlight the role of hybridization. Furthermore, analysis of intra-individual genetic diversity suggests one or several allopolyploid origins for Mediterranean Romulea. Four taxa (R. assumptionis, R. revelieri, R. ligustica, R. rollii) are consistently well differentiated across nuclear and plastid datasets, supporting their recognition as distinct species. In contrast, the widespread species R. ramiflora and R. columnae contain well-differentiated groups that may represent cryptic speciation. Several other taxa, including R. x melitensis, R. corsica, and R. bulbocodium, exhibit genomic signatures consistent with hybrid origins. Plastid and nuclear variation patterns are consistent with a hypothesis of rapid radiation in the Tyrrhenian region. These results provide a primary genomic framework for the integrative taxonomy of Romulea.

Genetic Variation↗

PubMed2025

Deazapurine Amide-Bond Synthetases: a New Family of Amide-Bond-Forming Enzymes Driving the Diversity of Peptidyl Deazapurine Natural Products.

Amide bond-forming enzymes play a crucial role in generating structural diversity in natural products by assembling them from relatively simple precursors. Two distinct types of standalone amid-bond-forming enzymes are commonly involved in natural product biosynthesis, including ATP-grasp enzymes and amide bond synthetases. Here, we report a new family of amide bond synthetases that catalyze amide bond formation between deazapurine as the sole carboxylic acid substrate and various amine substrates, which we have designated as deazapurine amide bond synthetases (DABS). This evolutionarily related enzyme family plays a central role in diversifying the structures of peptidyl deazapurine natural products. Our gene mining analysis reveals that most DABS-associated biosynthetic gene clusters (BGCs) remain cryptic. Therefore, systematic characterization of these cryptic BGCs holds great potential for discovering novel peptidyl deazapurine natural products with diverse biological activities.

Biological Products↗

PubMed2024

Metagenomic insights and biosynthetic potential of Candidatus Entotheonella symbiont associated with Halichondria marine sponges.

Korea, being surrounded by the sea, provides a rich habitat for marine sponges, which have been a prolific source of bioactive natural products. Although a diverse array of structurally novel natural products has been isolated from Korean marine sponges, their biosynthetic origins remain largely unknown. To explore the biosynthetic potential of Korean marine sponges, we conducted metagenomic analyses of sponges inhabiting the East Sea of Korea. This analysis revealed a symbiotic association of Candidatus Entotheonella bacteria with Halichondria sponges. Here, we report a new chemically rich Entotheonella variant, which we named Ca. Entotheonella halido. Remarkably, this symbiont makes up 69% of the microbial community in the sponge Halichondira dokdoensis. Genome-resolved metagenomics enabled us to obtain a high-quality Ca. E. halido genome, which represents the largest (12 Mb) and highest quality among previously reported Entotheonella genomes. We also identified the biosynthetic gene cluster (BGC) of the known sponge-derived Halicylindramides from the Ca. E. halido genome, enabling us to determine their biosynthetic origin. This new symbiotic association expands the host diversity and biosynthetic potential of metabolically talented bacterial genus Ca. Entotheonella symbionts.IMPORTANCEOur study reports the discovery of a new bacterial symbiont Ca. Entotheonella halido associated with the Korean marine sponge Halichondria dokdoensis. Using genome-resolved metagenomics, we recovered a high-quality Ca. E. halido MAG (Metagenome-Assembled Genome), which represents the largest and most complete Ca. Entotheonella MAG reported to date. Pangenome and BGC network analyses revealed a remarkably high BGC diversity within the Ca. Entotheonella pangenome, with almost no overlapping BGCs between different MAGs. The cryptic and genetically unique BGCs present in the Ca. Entotheonella pangenome represents a promising source of new bioactive natural products.

Animals↗

PubMed2026

Exploring shotgun metagenomic data to detect microeukaryotic pathogens in wildlife.

BACKGROUND: Microeukaryotic parasites of the intestinal tract are an understudied group of organisms that infect humans and many other animals. Targeted sequencing methods focused on individual loci are usually employed for detection of these parasites, making comprehensive studies of microeukaryotic parasite diversity within hosts or other systems difficult. Exploratory approaches such as shotgun metagenomic sequencing to survey the diversity of microeukaryotic parasites in new and existing datasets are not well developed. RESULTS: Utilizing existing datasets from 12 goose fecal samples, we explored some of the benefits and challenges of using shotgun metagenome sequencing to detect microeukaryotic parasites. We demonstrated the importance of careful curation of read classification data to avoid erroneously linking pathogens to hosts or environments as unsupported classifications were common in the data and varied widely depending on analysis parameters. However, we were able to establish strong support for the presence of sequences of Eimeria and Enterocytozoon bieneusi. In addition, examination of trichomonad reads indicated that parasite reads mapping to human pathogens unlikely to colonize geese may in fact represent cryptic microeukaryotic species that are not included in existing curated databases opening new potential avenues of study. CONCLUSIONS: Taken together these findings support the idea that exploring microeukaryotic parasite diversity within shotgun metagenomic datasets can be beneficial to our understanding of the presence and diversity of these organisms in wildlife hosts.

Animals↗

PubMed2026

From sequence space to ecological function: microbiome-derived antimicrobial peptides as community effectors and therapeutic leads.

Antimicrobial peptide research has long centred on host defence molecules, yet microbiomes themselves encode a diverse and increasingly important repertoire of peptide-based antimicrobials. These microbiome-derived antimicrobial peptides include bacteriocins, ribosomally synthesised and post-translationally modified peptides, cryptic short open reading frame-encoded peptides, embedded antimicrobial regions within larger proteins, and selected peptide antibiotics recovered from human, animal, plant and environmental microbiomes. Recent advances in genome mining, metagenomics, and machine learning have greatly expanded the scale of discovery, moving the field from a handful of landmark exemplars to large candidate catalogues spanning the global microbiome. In the clearest cases, these molecules are not only anti-infective leads but ecological effectors: they mediate microbial competition, enforce colonisation resistance, and influence community structure within densely occupied niches. The present review synthesises the field across discovery classes, microbiome sources, ecological roles, and translational bottlenecks, emphasizing a central limitation of the field: candidate catalogues are expanding at extraordinary scale, while evidence for native expression, producer assignment, ecological function, and in vivo relevance remains limited for the vast majority of predicted molecules. Progress will depend on workflows that connect sequence level prediction to biological context through expression support, producer assignment, community level validation, and perturbation-based approaches that distinguish ecological association from causal function. Microbiome-derived antimicrobial peptides are best understood not only as promising therapeutic leads, but also as molecular mediators of microbial social life whose ecological origins are central to their interpretation and future application.

Microbiota↗

PubMed2024

Oceanic islands act as drivers for the genetic diversity of marine species: Cardita calyculata (Linnaeus, 1758) in the NE Atlantic as a case-study.

Geographic distribution, as well as evolutionary and biogeographic processes and patterns of marine invertebrate benthic species are strongly shaped by dispersal ability during the life cycle. Remote oceanic islands lie at the brink of complex biotic and abiotic interactions which have significantly influenced the biodiversity patterns we see today. The interaction between geological environmental change and taxon-specific dispersal modes can influence species evolutionary patterns, eventually delimiting species-specific biogeographic regions. In this study, we compare the population genetic patterns of the marine bivalve Cardita calyculata in the northeast Atlantic, discussing the role of Macaronesian islands during past climatic cycles. The genetic structure and diversity patterns were outlined based on SSR-GBAS loci of 165 individuals and on the mitochondrial COI marker of 22 individuals from the Canary Islands, Madeira, Azores and the Mediterranean. The highly structured genetic pattern found among regions and within archipelagos suggests the central role of oceanic islands in promoting the divergence of the species in both the NE Atlantic and the Mediterranean. The high degree of divergence in the COI dataset (> 7%) suggests the existence of potential cryptic speciation that needs to be further explored with a more comprehensive sampling. Such patterns are only congruent with a scenario where C. calyculata populations were maintained during glacial/interglacial cycles, supporting the role of the studied archipelagos as drivers of diversity for marine biota. We stress the importance of developing studies for species with various life history and dispersal modes. In such a way, a more profound understanding of the biogeographic and evolutionary significance of oceanic islands can catalyse directed conservation efforts, especially in the context of the ongoing climate crisis.

Animals↗